ICM-Chemist-Pro User Guide v.3.7-2a

Table of contents

1 How To Guides and Videos

1.1 ICM-Browser How To Guide

1.2 ICM-Browser-Pro How To Guide

1.3 ActiveICM How To Guide - Create 3D Molecular Documents for the Web and PowerPoint

1.4 ICM-Chemist How To Guide

1.5 ICM-Chemist-Pro How To Guide

2 Getting Started

2.1 How to Use the Graphical Display

2.2 Making Selections

2.3 Menu Option Guide

2.4 Tab Guide

3 Working with Protein Structures

3.1 Searching the PDB

3.2 Converting PDB Files Into ICM Objects

3.3 How to Display the Ligand Binding Pocket Surface and Neighboring Residues.

3.4 How to Display Hydrogen Bonds

4 Molecular Graphics

4.1  Molecule Representation

4.2  Meshes - Surface - Grobs

4.3  Coloring

4.4  Lighting

4.5  Labeling and Annotation

4.6  Display Distances and Angles

4.7  Graphics Effects

4.8  Graphics Shortcuts

4.9  Molecule Move Buttons

4.10 Clipping Tools

4.11 Graphic Layers

4.12 Make High Quality Publication Images

5 Molecular Animations, Slides, and Documents

5.1 Molecular Animations and Transitions

5.2 Making Slides

5.3 How to View and Navigate Slides

5.4 How to Edit Slides

5.5 How to Add Smooth Blending and Transition Effects Between Slides

5.6 How to Make Molecular Documents - Link HTML Text to Slides

6 ActiveICM

6.1 How to Embed in Microsoft PowerPoint 2003

6.2 How to Embed in Microsoft PowerPoint 2007

6.3 Embed in Web Browser

6.4 How to Use ActiveICM in PowerPoint

6.5 How to Change ActiveICM Component Properties

6.6 Advanced use of activeICM: Macros to direct visualisation changes

6.7 Background Images

7 Movie Making

7.1 Screen-grabbing Movie

7.2 View-Defined Movie Making

8 Protein Structure Analysis

8.1  Find Related Chains

8.2  Calculate RMSD

8.3  Contact Areas

8.4  Identify Closed Cavities

8.5  Surface Area

8.6  Measure Distances

8.7  Planar Angle

8.8  Dihedral Angle

8.9  Ramachandran Plot Interactive

8.10 Export Ramachandran Plot

9 Protein Superposition

9.1 Select Proteins for Superposition

9.2 Superimpose Button

9.3 Superimpose by 3D

9.4 Superimpose Multiple Proteins

9.5 Arrange as Grid

10 Crystallographic Analysis

10.1  Crystallographic Neighbor

10.2  Crystallographic Cell

10.3  Biomolecule Generator

10.4  Get Electron Density Map

10.5  Map's Original Cell

10.6  Contour Electron Density Map

10.7  Convert Xray Density to Grid

10.8  Protein Health

10.9  Local Flexibility

10.10 Protein-Protein Interface Prediction

10.11 Identfy Ligand Pockets

11 Cheminformatics

11.1  Reading Chemical Structures

11.2  Working with Chemical Spreadsheets.

11.3  Molecular Editor

11.4  How to extract a 2D sketch of a ligand in complex with a PDB strcture.

11.5  Convert Chemicals to 3D

11.6  Saving Chemical Structures and Images

11.7  Export to Excel

11.8  IUPAC Chemical Nomenclature

11.9  Chemical Search

11.10 Pharmacophore Drawing and Searching

11.11 Find and Replace

11.12 Generating Chemical Fragments

11.13 Molcart

12 Chemistry Menu

12.1  Calculate Properties

12.2  Standardize Table

12.3  Annotate By Substructure

12.4  Align/Color by 2D Scaffold

12.5  Set Formal Charges

12.6  Convert

12.7  Build Prediction Model

12.8  Predict

12.9  Generate 3D Conformers

12.10 Generate Tautomers

12.11 Generate Stereoismers

12.12 Cluster Set

12.13 PCA Analysis

12.14 Compare Two Sets

12.15 Merge Two Sets

12.16 Select Duplicates

12.17 Combinatorial Chemistry

12.18 Substructure Superposition

12.19 Atomic Property Field Superposition

13 How to use the 3D Interactive Ligand Editor

13.1  Setup Ligand and Receptor

13.2  Ligand-Editor-Preferences

13.3  Pocket Display Options

13.4  Display Hydrogen Bonds

13.5  Display Atomic Energy Circles

13.6  Re-Dock and Minimize Ligand

13.7  How to Save Ligand Receptor Complex as PDB

13.8  Edit Ligand

13.9  Insert a linker

13.10 Find Best Replacement Group

13.11 Impose Restraint (tethers) To Ligand Atoms

13.12 Dock to Atomic Property Fields

14 Working with Tables

14.1 Standard ICM Tables

14.2 Molecular Tables

14.3 Insert Interactive Objects into Table Cell

14.4 Plotting Table Data

14.5 Principal Component Analysis

14.6 Learn and Predict

14.7 Cluster

15 Working with Local Databases

15.1 How to make a local database.

15.2 Browse Database

15.3 Edit Database

15.4 Query Local Database

16 Tutorials

16.1 Graphics Tutorials

16.2 Cheminformatics Tutorials

16.3 How to Work with the ICM 3D Ligand Editor